@article{GoettschBeerenwinkelDengetal.2021, author = {Goettsch, Winfried and Beerenwinkel, Niko and Deng, Li and D{\"o}lken, Lars and Dutilh, Bas E. and Erhard, Florian and Kaderali, Lars and Kleist, Max von and Marquet, Roland and Matthijnssens, Jelle and McCallin, Shawna and McMahon, Dino and Rattei, Thomas and Van Rij, Ronald P. and Robertson, David L. and Schwemmle, Martin and Stern-Ginossar, Noam and Marz, Manja}, title = {ITN—VIROINF: Understanding (harmful) virus-host interactions by linking virology and bioinformatics}, series = {Viruses}, volume = {13}, journal = {Viruses}, number = {5}, issn = {1999-4915}, doi = {10.3390/v13050766}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-236687}, year = {2021}, abstract = {Many recent studies highlight the fundamental importance of viruses. Besides their important role as human and animal pathogens, their beneficial, commensal or harmful functions are poorly understood. By developing and applying tailored bioinformatical tools in important virological models, the Marie Skłodowska-Curie Initiative International Training Network VIROINF will provide a better understanding of viruses and the interaction with their hosts. This will open the door to validate methods of improving viral growth, morphogenesis and development, as well as to control strategies against unwanted microorganisms. The key feature of VIROINF is its interdisciplinary nature, which brings together virologists and bioinformaticians to achieve common goals.}, language = {en} } @phdthesis{Kuen2017, author = {Kuen, Janina}, title = {Influence of 3D tumor cell/fibroblast co-culture on monocyte differentiation and tumor progression in pancreatic cancer}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-156226}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2017}, abstract = {Pancreatic cancer (PC) remains one of the most challenging solid tumors to treat with a high unmet medical need as patients poorly respond to standard-of-care-therapies. Prominent desmoplastic reaction involving cancer-associated fibroblasts (CAFs) and the immune cells in the tumor microenvironment (TME) and their cross-talk play a significant role in tumor immune escape and progression. To identify the key cellular mechanisms induce an immunosuppressive tumor microenvironment, we established 3D co-culture model with pancreatic cancer cells, CAFs, monocyte as well as T cells. Using this model, we analysed the influence of tumor cells and fibroblasts on monocytes and their immune suppressive phenotype. Phenotypic characterization of the monocytes after 3D co-culture with tumor/fibroblast spheroids was performed by analysing the expression of defined cell surface markers and soluble factors. Functionality of these monocytes and their ability to influence T cell phenotype and proliferation was investigated. 3D co-culture of monocytes with pancreatic cancer cells and fibroblasts induced the production of immunosuppressive cytokines which are known to promote polarization of M2 like macrophages and myeloid derived suppressive cells (MDSCs). These co-culture spheroid polarized monocyte derived macrophages (MDMs) were poorly differentiated and had an M2 phenotype. The immunosuppressive function of these co-culture spheroids polarized MDMs was demonstrated by their ability to inhibit autologous CD4+ and CD8+ T cell activation and proliferation in vitro, which we could partially reverse by 3D co-culture spheroid treatment with therapeutic molecules that are able to re-activate spheroid polarized MDMs or block immune suppressive factors such as Arginase-I. In conclusion, we generated a physiologically relevant 3D co-culture model, which can be used as a promising tool to study complex cell-cell interactions between different cell types within the tumor microenvironment and to support drug screening and development. In future, research focused on better understanding of resistance mechanisms to existing cancer immunotherapies will help to develop new therapeutic strategies in order to combat cancer.}, subject = {monocyte}, language = {en} } @phdthesis{Froehlich2018, author = {Fr{\"o}hlich, Monika Gabriele}, title = {Die Bedeutung von CD28 vermittelter Kostimulation f{\"u}r CD8 T-Zell-Ged{\"a}chtnisreaktionen}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-158791}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2018}, abstract = {Immunologische Ged{\"a}chtnisreaktionen sind die Grundlage um wiederkehrende Erreger schnell und effizient zu bek{\"a}mpfen und um einen Impfschutz zu generieren. Das zellvermittelte Ged{\"a}chtnis wird unter anderem durch CD8 Ged{\"a}chtnis-T-Zellen aufgebaut, welche vor allem im Kontext von Immunreaktionen gegen intrazellul{\"a}rer Erreger vonn{\"o}ten sind, um bei Reinfektion mit den Erregerst{\"a}mmen einen schnellen Schutz zu gew{\"a}hrleisten. Ein detailliertes Wissen {\"u}ber die Generierung, Kontrolle und Reaktivierung der Ged{\"a}chtniszellen ist n{\"u}tzlich, um Ged{\"a}chtnisreaktionen verstehen und lenken zu k{\"o}nnen. Durch die Entdeckung des TZR und CD28 wurden Meilensteine f{\"u}r das Verst{\"a}ndnis der T-Zellaktivierung gelegt und die Grundlage geschaffen, CD8 Ged{\"a}chtnisreaktionen zu verstehen. Auch wenn f{\"u}r prim{\"a}re Immunreaktionen die „2-Signal-Theorie" lange als erwiesen gilt, so blieb die Rolle der Kostimulation f{\"u}r Ged{\"a}chtnisreaktionen lange umstritten. In dieser Arbeit wurden verschiedene methodische Herangehensweisen verwendet, mit denen durchgehend die Bedeutung von CD28 vermittelter Kostimulation f{\"u}r immunologische CD8 T-Zell-Ged{\"a}chtnisreaktionen nachgewiesen wurde. CD28 blockierende Antik{\"o}rper und CD28 induzierbar deletierbare Mauslinien wurden im Modellinfektionssystem mit Ovalbumin produzierenden Listeria monocytogenes zur Analyse der Prim{\"a}r- und Sekund{\"a}rantworten verwendet. Mit diesen Methoden konnte eine Beeintr{\"a}chtigung der Expansion von CD8 Ged{\"a}chtniszellen in Abwesenheit von CD28 bewiesen werden. Weiterhin werden Effektorfunktionen wie Degranulation und Produktion von IFN-γ w{\"a}hrend der Sekund{\"a}rinfektion in Abwesenheit von Kostimulation eingeschr{\"a}nkt. Mit Hilfe von Experimenten, bei denen CD28 suffizienten M{\"a}usen eine geringe Anzahl an naiven, antigenspezifischen, CD28 deletierbaren CD8 T-Zellen transferiert wurden, wurde die Bedeutung der Kostimulation f{\"u}r die Expansion von Ged{\"a}chtniszellen best{\"a}tigt, jedoch konnte {\"u}berraschenderweise auch ein Anstieg der Effektorfunktionen in Abwesenheit von CD28 sowohl w{\"a}hrend der Prim{\"a}r- als auch der Sekund{\"a}rantwort dokumentiert werden. Diese zur globalen Blockade bzw. Deletion widerspr{\"u}chlichen Ergebnisse lassen eine Beteiligung anderer CD28 abh{\"a}ngiger Zelltypen an der Induktion der Effektorfunktionen der CD8 T-Zellen plausibel erscheinen, wie zum Beispiel Einfl{\"u}sse von T-Helferzellen, welche die Effektorfunktionen positiv verst{\"a}rken, solange sie selbst Kostimulationssignale empfangen k{\"o}nnen. Weiterhin konnte gezeigt werden, dass sich Ged{\"a}chtniszellen an den CD28 defizienten Ph{\"a}notyp - eine CD28 intakte immunologische Umgebung vorausgesetzt - adaptieren k{\"o}nnen, wenn ausreichend Zeit nach Deletion und vor Sekund{\"a}rinfektion verstreichen konnte.}, subject = {Antigen CD28}, language = {de} } @article{SchneiderCoronaSpoeringetal.2016, author = {Schneider, Anna and Corona, Angela and Sp{\"o}ring, Imke and Jordan, Mareike and Buchholz, Bernd and Maccioni, Elias and Di Santo, Roberto and Bodem, Jochen and Tramontano, Enzo and W{\"o}hrl, Birgitta M.}, title = {Biochemical characterization of a multi-drug resistant HIV-1 subtype AG reverse transcriptase: antagonism of AZT discrimination and excision pathways and sensitivity to RNase H inhibitors}, series = {Nucleic Acids Research}, volume = {44}, journal = {Nucleic Acids Research}, number = {5}, doi = {10.1093/nar/gkw060}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166423}, pages = {2310-2322}, year = {2016}, abstract = {We analyzed a multi-drug resistant (MR) HIV-1 reverse transcriptase (RT), subcloned from a patient-derived subtype CRF02_AG, harboring 45 amino acid exchanges, amongst them four thymidine analog mutations (TAMs) relevant for high-level AZT (azidothymidine) resistance by AZTMP excision (M41L, D67N, T215Y, K219E) as well as four substitutions of the AZTTP discrimination pathway (A62V, V75I, F116Y and Q151M). In addition, K65R, known to antagonize AZTMP excision in HIV-1 subtype B was present. Although MR-RT harbored the most significant amino acid exchanges T215Y and Q151M of each pathway, it exclusively used AZTTP discrimination, indicating that the two mechanisms are mutually exclusive and that the Q151M pathway is obviously preferred since it confers resistance to most nucleoside inhibitors. A derivative was created, additionally harboring the TAM K70R and the reversions M151Q as well as R65K since K65R antagonizes excision. MR-R65K-K70R-M151Q was competent of AZTMP excision, whereas other combinations thereof with only one or two exchanges still promoted discrimination. To tackle the multi-drug resistance problem, we tested if the MR-RTs could still be inhibited by RNase H inhibitors. All MR-RTs exhibited similar sensitivity toward RNase H inhibitors belonging to different inhibitor classes, indicating the importance of developing RNase H inhibitors further as anti-HIV drugs.}, language = {en} } @article{HennigMichalskiRutkowskietal.2018, author = {Hennig, Thomas and Michalski, Marco and Rutkowski, Andrzej J. and Djakovic, Lara and Whisnant, Adam W. and Friedl, Marie-Sophie and Jha, Bhaskar Anand and Baptista, Marisa A. P. and L'Hernault, Anne and Erhard, Florian and D{\"o}lken, Lars and Friedel, Caroline C.}, title = {HSV-1-induced disruption of transcription termination resembles a cellular stress response but selectively increases chromatin accessibility downstream of genes}, series = {PLoS Pathogens}, volume = {14}, journal = {PLoS Pathogens}, number = {3}, doi = {10.1371/journal.ppat.1006954}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-176350}, pages = {e1006954}, year = {2018}, abstract = {Lytic herpes simplex virus 1 (HSV-1) infection triggers disruption of transcription termination (DoTT) of most cellular genes, resulting in extensive intergenic transcription. Similarly, cellular stress responses lead to gene-specific transcription downstream of genes (DoG). In this study, we performed a detailed comparison of DoTT/DoG transcription between HSV-1 infection, salt and heat stress in primary human fibroblasts using 4sU-seq and ATAC-seq. Although DoTT at late times of HSV-1 infection was substantially more prominent than DoG transcription in salt and heat stress, poly(A) read-through due to DoTT/DoG transcription and affected genes were significantly correlated between all three conditions, in particular at earlier times of infection. We speculate that HSV-1 either directly usurps a cellular stress response or disrupts the transcription termination machinery in other ways but with similar consequences. In contrast to previous reports, we found that inhibition of Ca\(^{2+}\) signaling by BAPTA-AM did not specifically inhibit DoG transcription but globally impaired transcription. Most importantly, HSV-1-induced DoTT, but not stress-induced DoG transcription, was accompanied by a strong increase in open chromatin downstream of the affected poly(A) sites. In its extent and kinetics, downstream open chromatin essentially matched the poly(A) read-through transcription. We show that this does not cause but rather requires DoTT as well as high levels of transcription into the genomic regions downstream of genes. This raises intriguing new questions regarding the role of histone repositioning in the wake of RNA Polymerase II passage downstream of impaired poly(A) site recognition.}, language = {en} } @article{WhisnantJuergesHennigetal.2020, author = {Whisnant, Adam W. and J{\"u}rges, Christopher S. and Hennig, Thomas and Wyler, Emanuel and Prusty, Bhupesh and Rutkowski, Andrzej J. and L'hernault, Anne and Djakovic, Lara and G{\"o}bel, Margarete and D{\"o}ring, Kristina and Menegatti, Jennifer and Antrobus, Robin and Matheson, Nicholas J. and K{\"u}nzig, Florian W. H. and Mastrobuoni, Guido and Bielow, Chris and Kempa, Stefan and Liang, Chunguang and Dandekar, Thomas and Zimmer, Ralf and Landthaler, Markus and Gr{\"a}sser, Friedrich and Lehner, Paul J. and Friedel, Caroline C. and Erhard, Florian and D{\"o}lken, Lars}, title = {Integrative functional genomics decodes herpes simplex virus 1}, series = {Nature Communications}, volume = {11}, journal = {Nature Communications}, doi = {10.1038/s41467-020-15992-5}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-229884}, year = {2020}, abstract = {The predicted 80 open reading frames (ORFs) of herpes simplex virus 1 (HSV-1) have been intensively studied for decades. Here, we unravel the complete viral transcriptome and translatome during lytic infection with base-pair resolution by computational integration of multi-omics data. We identify a total of 201 transcripts and 284 ORFs including all known and 46 novel large ORFs. This includes a so far unknown ORF in the locus deleted in the FDA-approved oncolytic virus Imlygic. Multiple transcript isoforms expressed from individual gene loci explain translation of the vast majority of ORFs as well as N-terminal extensions (NTEs) and truncations. We show that NTEs with non-canonical start codons govern the subcellular protein localization and packaging of key viral regulators and structural proteins. We extend the current nomenclature to include all viral gene products and provide a genome browser that visualizes all the obtained data from whole genome to single-nucleotide resolution. Here, using computational integration of multi-omics data, the authors provide a detailed transcriptome and translatome of herpes simplex virus 1 (HSV-1), including previously unidentified ORFs and N-terminal extensions. The study also provides a HSV-1 genome browser and should be a valuable resource for further research.}, language = {en} } @article{RasaNoraKrukleHenningetal.2018, author = {Rasa, Santa and Nora-Krukle, Zaiga and Henning, Nina and Eliassen, Eva and Shikova, Evelina and Harrer, Thomas and Scheibenbogen, Carmen and Murovska, Modra and Prusty, Bhupesh K.}, title = {Chronic viral infections in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS)}, series = {Journal of Translational Medicine}, volume = {16}, journal = {Journal of Translational Medicine}, number = {268}, doi = {10.1186/s12967-018-1644-y}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-224960}, pages = {1-25}, year = {2018}, abstract = {Background and main text: Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a complex and controversial clinical condition without having established causative factors. Increasing numbers of cases during past decade have created awareness among patients as well as healthcare professionals. Chronic viral infection as a cause of ME/CFS has long been debated. However, lack of large studies involving well-designed patient groups and validated experimental set ups have hindered our knowledge about this disease. Moreover, recent developments regarding molecular mechanism of pathogenesis of various infectious agents cast doubts over validity of several of the past studies. Conclusions: This review aims to compile all the studies done so far to investigate various viral agents that could be associated with ME/CFS. Furthermore, we suggest strategies to better design future studies on the role of viral infections in ME/CFS.}, language = {en} } @phdthesis{Eckert2023, author = {Eckert, Ina-Nathalie}, title = {Molecular markers of myeloid-derived suppressor cells and their functional role for homing and in disease models in mice}, doi = {10.25972/OPUS-31997}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-319974}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2023}, abstract = {MDSCs are suppressive immune cells with a high relevance in various pathologies including cancer, autoimmunity, and chronic infections. Surface marker expression of MDSCs resembles monocytes and neutrophils which have immunostimulatory functions instead of suppressing T cells. Therefore, finding specific surface markers for MDSCs is important for MDSC research and therapeutic MDSC manipulation. In this study, we analyzed if the integrin VLA-1 has the potential as a novel MDSC marker. VLA-1 was expressed by M-MDSCs but not by G-MDSCs as well as by Teff cells. VLA-1 deficiency did not impact iNOS expression, the distribution of M-MDSC and G-MDSC subsets, and the suppressive capacity of MDSCs towards na{\"i}ve and Teff cells in vitro. In mice, VLA-1 had no effect on the homing capability of MDSCs to the spleen, which is a major reservoir for MDSCs. Since the splenic red pulp contains collagen IV and VLA-1 binds collagen IV with a high affinity, we found MDSCs and Teff cells in this area as expected. We showed that T cell suppression in the spleen, indicated by reduced T cell recovery and proliferation as well as increased apoptosis and cell death, partially depended on VLA-1 expression by the MDSCs. In a mouse model of multiple sclerosis, MDSC injection prior to disease onset led to a decrease of the disease score, and this effect was significantly reduced when MDSCs were VLA-1 deficient. The expression of Sema7A by Teff cells, a ligand for VLA-1 which is implicated in negative T cell regulation, resulted in a slightly stronger Teff cell suppression by MDSCs compared to Sema7A deficient T cells. Live cell imaging and intravital 2-photon microscopy showed that the interaction time of MDSCs and Teff cells was shorter when MDSCs lacked VLA 1 expression, however VLA-1 expression had no impact on MDSC mobility. Therefore, the VLA-1-dependent interaction of MDSC and Teff cells on collagen IV in the splenic red pulp is implicated MDSC-mediated Teff cell suppression.}, subject = {Immunologie}, language = {en} } @article{EderHollmannMandasarietal.2022, author = {Eder, Sascha and Hollmann, Claudia and Mandasari, Putri and Wittmann, Pia and Schumacher, Fabian and Kleuser, Burkhard and Fink, Julian and Seibel, J{\"u}rgen and Schneider-Schaulies, J{\"u}rgen and Stigloher, Christian and Beyersdorf, Niklas and Dembski, Sofia}, title = {Synthesis and characterization of ceramide-containing liposomes as membrane models for different T cell subpopulations}, series = {Journal of Functional Biomaterials}, volume = {13}, journal = {Journal of Functional Biomaterials}, number = {3}, issn = {2079-4983}, doi = {10.3390/jfb13030111}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-286130}, year = {2022}, abstract = {A fine balance of regulatory (T\(_{reg}\)) and conventional CD4\(^+\) T cells (T\(_{conv}\)) is required to prevent harmful immune responses, while at the same time ensuring the development of protective immunity against pathogens. As for many cellular processes, sphingolipid metabolism also crucially modulates the T\(_{reg}\)/T\(_{conv}\) balance. However, our understanding of how sphingolipid metabolism is involved in T cell biology is still evolving and a better characterization of the tools at hand is required to advance the field. Therefore, we established a reductionist liposomal membrane model system to imitate the plasma membrane of mouse T\(_{reg}\) and T\(_{conv}\) with regards to their ceramide content. We found that the capacity of membranes to incorporate externally added azide-functionalized ceramide positively correlated with the ceramide content of the liposomes. Moreover, we studied the impact of the different liposomal preparations on primary mouse splenocytes in vitro. The addition of liposomes to resting, but not activated, splenocytes maintained viability with liposomes containing high amounts of C\(_{16}\)-ceramide being most efficient. Our data thus suggest that differences in ceramide post-incorporation into T\(_{reg}\) and T\(_{conv}\) reflect differences in the ceramide content of cellular membranes.}, language = {en} } @article{GeigerDiesendorfRolletal.2023, author = {Geiger, Nina and Diesendorf, Viktoria and Roll, Valeria and K{\"o}nig, Eva-Maria and Obernolte, Helena and Sewald, Katherina and Breidenbach, Julian and Pillaiyar, Thanigaimalai and G{\"u}tschow, Michael and M{\"u}ller, Christa E. and Bodem, Jochen}, title = {Cell type-specific anti-viral effects of novel SARS-CoV-2 main protease inhibitors}, series = {International Journal of Molecular Sciences}, volume = {24}, journal = {International Journal of Molecular Sciences}, number = {4}, issn = {1422-0067}, doi = {10.3390/ijms24043972}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-304034}, year = {2023}, abstract = {Recently, we have described novel pyridyl indole esters and peptidomimetics as potent inhibitors of the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) main protease. Here, we analysed the impact of these compounds on viral replication. It has been shown that some antivirals against SARS-CoV-2 act in a cell line-specific way. Thus, the compounds were tested in Vero, Huh-7, and Calu-3 cells. We showed that the protease inhibitors at 30 µM suppress viral replication by up to 5 orders of magnitude in Huh-7 cells, while in Calu-3 cells, suppression by 2 orders of magnitude was achieved. Three pyridin-3-yl indole-carboxylates inhibited viral replication in all cell lines, indicating that they might repress viral replication in human tissue as well. Thus, we investigated three compounds in human precision-cut lung slices and observed donor-dependent antiviral activity in this patient-near system. Our results provide evidence that even direct-acting antivirals may act in a cell line-specific manner.}, language = {en} }